python main.py Fig1D_AID-BE5max-NG-rep2_S98_L001_R1_001.fastq.gz out/Fig1D_AID-BE5max-NG-rep2_S98_L001_R1_001 -a GGGGACTGCCGTGCCGGGCGGGAGACCGCCATGGCGACCCTGGAAAAGCTGATGAAGGCCTTCGAGTCCCTCAAGTCCTTC(YAR)CAACAGCCGCCACCGCCGCCGCCGCCGCCGCCGCCTCCTCAGCTTCCTCAGCCGCCGCCGCAGGCACAGCCGCTGCTGCCTCAGCCGCAGCC --no_trim
python main.py Fig1D_AID-BE5max-NG-rep3_S62_L001_R1_001.fastq.gz out/Fig1D_AID-BE5max-NG-rep3_S62_L001_R1_001 -a GGGGACTGCCGTGCCGGGCGGGAGACCGCCATGGCGACCCTGGAAAAGCTGATGAAGGCCTTCGAGTCCCTCAAGTCCTTC(YAR)CAACAGCCGCCACCGCCGCCGCCGCCGCCGCCGCCTCCTCAGCTTCCTCAGCCGCCGCCGCAGGCACAGCCGCTGCTGCCTCAGCCGCAGCC --no_trim
python main.py Fig1D_BE4max-NG-rep1_S1_L001_R1_001.fastq.gz out/Fig1D_BE4max-NG-rep1_S1_L001_R1_001 -a GGGGACTGCCGTGCCGGGCGGGAGACCGCCATGGCGACCCTGGAAAAGCTGATGAAGGCCTTCGAGTCCCTCAAGTCCTTC(YAR)CAACAGCCGCCACCGCCGCCGCCGCCGCCGCCGCCTCCTCAGCTTCCTCAGCCGCCGCCGCAGGCACAGCCGCTGCTGCCTCAGCCGCAGCC --no_trim
python main.py Fig1D_BE4max-NG-rep2_S89_L001_R1_001.fastq.gz out/Fig1D_BE4max-NG-rep2_S89_L001_R1_001 -a GGGGACTGCCGTGCCGGGCGGGAGACCGCCATGGCGACCCTGGAAAAGCTGATGAAGGCCTTCGAGTCCCTCAAGTCCTTC(YAR)CAACAGCCGCCACCGCCGCCGCCGCCGCCGCCGCCTCCTCAGCTTCCTCAGCCGCCGCCGCAGGCACAGCCGCTGCTGCCTCAGCCGCAGCC --no_trim
python main.py Fig1D_BE4max-NG-rep3_S53_L001_R1_001.fastq.gz out/Fig1D_BE4max-NG-rep3_S53_L001_R1_001 -a GGGGACTGCCGTGCCGGGCGGGAGACCGCCATGGCGACCCTGGAAAAGCTGATGAAGGCCTTCGAGTCCCTCAAGTCCTTC(YAR)CAACAGCCGCCACCGCCGCCGCCGCCGCCGCCGCCTCCTCAGCTTCCTCAGCCGCCGCCGCAGGCACAGCCGCTGCTGCCTCAGCCGCAGCC --no_trim
python main.py Fig1D_BE5max-NG-rep1_S3_L001_R1_001.fastq.gz out/Fig1D_BE5max-NG-rep1_S3_L001_R1_001 -a GGGGACTGCCGTGCCGGGCGGGAGACCGCCATGGCGACCCTGGAAAAGCTGATGAAGGCCTTCGAGTCCCTCAAGTCCTTC(YAR)CAACAGCCGCCACCGCCGCCGCCGCCGCCGCCGCCTCCTCAGCTTCCTCAGCCGCCGCCGCAGGCACAGCCGCTGCTGCCTCAGCCGCAGCC --no_trim
python main.py Fig1D_BE5max-NG-rep2_S91_L001_R1_001.fastq.gz out/Fig1D_BE5max-NG-rep2_S91_L001_R1_001 -a GGGGACTGCCGTGCCGGGCGGGAGACCGCCATGGCGACCCTGGAAAAGCTGATGAAGGCCTTCGAGTCCCTCAAGTCCTTC(YAR)CAACAGCCGCCACCGCCGCCGCCGCCGCCGCCGCCTCCTCAGCTTCCTCAGCCGCCGCCGCAGGCACAGCCGCTGCTGCCTCAGCCGCAGCC --no_trim
python main.py Fig1D_BE5max-NG-rep3_S55_L001_R1_001.fastq.gz out/Fig1D_BE5max-NG-rep3_S55_L001_R1_001 -a GGGGACTGCCGTGCCGGGCGGGAGACCGCCATGGCGACCCTGGAAAAGCTGATGAAGGCCTTCGAGTCCCTCAAGTCCTTC(YAR)CAACAGCCGCCACCGCCGCCGCCGCCGCCGCCGCCTCCTCAGCTTCCTCAGCCGCCGCCGCAGGCACAGCCGCTGCTGCCTCAGCCGCAGCC --no_trim
python main.py Fig1D_CDA1-BE4max-NG-rep1_S4_L001_R1_001.fastq.gz out/Fig1D_CDA1-BE4max-NG-rep1_S4_L001_R1_001 -a GGGGACTGCCGTGCCGGGCGGGAGACCGCCATGGCGACCCTGGAAAAGCTGATGAAGGCCTTCGAGTCCCTCAAGTCCTTC(YAR)CAACAGCCGCCACCGCCGCCGCCGCCGCCGCCGCCTCCTCAGCTTCCTCAGCCGCCGCCGCAGGCACAGCCGCTGCTGCCTCAGCCGCAGCC --no_trim
python main.py Fig1D_CDA1-BE4max-NG-rep2_S92_L001_R1_001.fastq.gz out/Fig1D_CDA1-BE4max-NG-rep2_S92_L001_R1_001 -a GGGGACTGCCGTGCCGGGCGGGAGACCGCCATGGCGACCCTGGAAAAGCTGATGAAGGCCTTCGAGTCCCTCAAGTCCTTC(YAR)CAACAGCCGCCACCGCCGCCGCCGCCGCCGCCGCCTCCTCAGCTTCCTCAGCCGCCGCCGCAGGCACAGCCGCTGCTGCCTCAGCCGCAGCC --no_trim
python main.py Fig1D_CDA1-BE4max-NG-rep3_S56_L001_R1_001.fastq.gz out/Fig1D_CDA1-BE4max-NG-rep3_S56_L001_R1_001 -a GGGGACTGCCGTGCCGGGCGGGAGACCGCCATGGCGACCCTGGAAAAGCTGATGAAGGCCTTCGAGTCCCTCAAGTCCTTC(YAR)CAACAGCCGCCACCGCCGCCGCCGCCGCCGCCGCCTCCTCAGCTTCCTCAGCCGCCGCCGCAGGCACAGCCGCTGCTGCCTCAGCCGCAGCC --no_trim
python main.py Fig1D_evoA-BE5max-NG-rep1_S19_L001_R1_001.fastq.gz out/Fig1D_evoA-BE5max-NG-rep1_S19_L001_R1_001 -a GGGGACTGCCGTGCCGGGCGGGAGACCGCCATGGCGACCCTGGAAAAGCTGATGAAGGCCTTCGAGTCCCTCAAGTCCTTC(YAR)CAACAGCCGCCACCGCCGCCGCCGCCGCCGCCGCCTCCTCAGCTTCCTCAGCCGCCGCCGCAGGCACAGCCGCTGCTGCCTCAGCCGCAGCC --no_trim
python main.py Fig1D_evoA-BE5max-NG-rep2_S107_L001_R1_001.fastq.gz out/Fig1D_evoA-BE5max-NG-rep2_S107_L001_R1_001 -a GGGGACTGCCGTGCCGGGCGGGAGACCGCCATGGCGACCCTGGAAAAGCTGATGAAGGCCTTCGAGTCCCTCAAGTCCTTC(YAR)CAACAGCCGCCACCGCCGCCGCCGCCGCCGCCGCCTCCTCAGCTTCCTCAGCCGCCGCCGCAGGCACAGCCGCTGCTGCCTCAGCCGCAGCC --no_trim
python main.py Fig1D_evoA-BE5max-NG-rep3_S71_L001_R1_001.fastq.gz out/Fig1D_evoA-BE5max-NG-rep3_S71_L001_R1_001 -a GGGGACTGCCGTGCCGGGCGGGAGACCGCCATGGCGACCCTGGAAAAGCTGATGAAGGCCTTCGAGTCCCTCAAGTCCTTC(YAR)CAACAGCCGCCACCGCCGCCGCCGCCGCCGCCGCCTCCTCAGCTTCCTCAGCCGCCGCCGCAGGCACAGCCGCTGCTGCCTCAGCCGCAGCC --no_trim
python main.py Fig1D_OFFevoA-BE5max-32NLS-NG-rep1_S93_L001_R1_001.fastq.gz out/Fig1D_OFFevoA-BE5max-32NLS-NG-rep1_S93_L001_R1_001 -a GGGGACTGCCGTGCCGGGCGGGAGACCGCCATGGCGACCCTGGAAAAGCTGATGAAGGCCTTCGAGTCCCTCAAGTCCTTC(YAR)CAACAGCCGCCACCGCCGCCGCCGCCGCCGCCGCCTCCTCAGCTTCCTCAGCCGCCGCCGCAGGCACAGCCGCTGCTGCCTCAGCCGCAGCC --no_trim
python main.py Fig1D_OFFevoA-BE5max-32NLS-NG-rep2_S189_L001_R1_001.fastq.gz out/Fig1D_OFFevoA-BE5max-32NLS-NG-rep2_S189_L001_R1_001 -a GGGGACTGCCGTGCCGGGCGGGAGACCGCCATGGCGACCCTGGAAAAGCTGATGAAGGCCTTCGAGTCCCTCAAGTCCTTC(YAR)CAACAGCCGCCACCGCCGCCGCCGCCGCCGCCGCCTCCTCAGCTTCCTCAGCCGCCGCCGCAGGCACAGCCGCTGCTGCCTCAGCCGCAGCC --no_trim
python main.py Fig1D_OFFevoA-BE5max-32NLS-NG-rep3_S285_L001_R1_001.fastq.gz out/Fig1D_OFFevoA-BE5max-32NLS-NG-rep3_S285_L001_R1_001 -a GGGGACTGCCGTGCCGGGCGGGAGACCGCCATGGCGACCCTGGAAAAGCTGATGAAGGCCTTCGAGTCCCTCAAGTCCTTC(YAR)CAACAGCCGCCACCGCCGCCGCCGCCGCCGCCGCCTCCTCAGCTTCCTCAGCCGCCGCCGCAGGCACAGCCGCTGCTGCCTCAGCCGCAGCC --no_trim
python main.py Fig1D_UT-rep1_S27_L001_R1_001.fastq.gz out/Fig1D_UT-rep1_S27_L001_R1_001 -a GGGGACTGCCGTGCCGGGCGGGAGACCGCCATGGCGACCCTGGAAAAGCTGATGAAGGCCTTCGAGTCCCTCAAGTCCTTC(YAR)CAACAGCCGCCACCGCCGCCGCCGCCGCCGCCGCCTCCTCAGCTTCCTCAGCCGCCGCCGCAGGCACAGCCGCTGCTGCCTCAGCCGCAGCC --no_trim
python main.py Fig1D_UT-rep2_S41_L001_R1_001.fastq.gz out/Fig1D_UT-rep2_S41_L001_R1_001 -a GGGGACTGCCGTGCCGGGCGGGAGACCGCCATGGCGACCCTGGAAAAGCTGATGAAGGCCTTCGAGTCCCTCAAGTCCTTC(YAR)CAACAGCCGCCACCGCCGCCGCCGCCGCCGCCGCCTCCTCAGCTTCCTCAGCCGCCGCCGCAGGCACAGCCGCTGCTGCCTCAGCCGCAGCC --no_trim
python main.py Fig1D_UT-rep3_S55_L001_R1_001.fastq.gz out/Fig1D_UT-rep3_S55_L001_R1_001 -a GGGGACTGCCGTGCCGGGCGGGAGACCGCCATGGCGACCCTGGAAAAGCTGATGAAGGCCTTCGAGTCCCTCAAGTCCTTC(YAR)CAACAGCCGCCACCGCCGCCGCCGCCGCCGCCGCCTCCTCAGCTTCCTCAGCCGCCGCCGCAGGCACAGCCGCTGCTGCCTCAGCCGCAGCC --no_trim
